Rhinolophus cognatushas a restricted distribution due to the relatively small size of the islands that it inhabits. It has an area of occupancy less than 500 km². The species has been reported from five independent locations and the number of subpopulations have probably declined as inferred from recent observations. The species has thus been classified as Endangered.

The Andaman Horseshoe Bat (Rhinolophus cognatus) is endemic to the Andaman Islands (Aul et al. 2014). It is not found in the Nicobar Islands (Bates and Harrison 1997, Aul 2006). Aul (2003) reported this species to be fairly widespread and found in the following major islands: North Andaman Island, Interview Island, Baratang, and Little Andaman; and small islands like Paget, Point and North Reef Islands. It was also caught in a mistnet at Saddle Peak in North Andaman Island at an altitude of ca 600 m asl (Aul 2003). However, the species was found to be absent in caves in North Andaman, Interview Island and Little Andaman Island during surveys in 2013-14 (R. Chakravarty pers. obs). The area of occupancy (AOO) for this species is estimated to be less than 500 km² based on known home ranges of approximately 5 km² (around the roost) of similar-sized Rhinolophids (Bontadina et al. 2002).

The abundance, population size and trends of this species are not known (Molur et al. 2002). The species was absent from previously known roosts at caves in North Andaman, Interview Island and Little Andaman during surveys in 2013-14 (R. Chakravarty pers. obs). This absence is not attributed to seasonality as the survey was done in approximately the same months as Aul (2003). It is therefore inferred that the number of subpopulations of this species is declining.

Rhinolophus cognatus predominantly roosts in caves but also in tree holes. Average colony size in caves appears to be less than 50 individuals (Aul 2006). It frequently shares its cave roosts with R. yunanensis and Hipposideros pomona (Aul 2003). An individual was observed hunting from a constant perch at the edge of moist lowland forest (R. Chakravarty pers. obs.) suggesting that it might be a perch hunter. Some individuals in a large limestone cave in Baratang were seen in torpor in the month of January when average minimum temperature was 18°C (R. Chakravarty pers. obs). It is certainly not as common and widespread as the sympatric R. yunanensis.

There are no direct conservation measures in place and the species is unprotected in the Indian Wildlife (Protection) Act, 1972. However, most of its current range falls within protected areas or areas with restricted access. Further studies are required to assess changes in the species’ distribution and population. Taxonomic studies must be undertaken to identify cryptic species (if any), particularly in Little Andaman Island. Since island species are sensitive to stochastic events, it is recommended that the species be accorded protection under the Wildlife (Protection) Act, 1972.